NM_006164.5(NFE2L2):c.445G>A (p.Gly149Ser) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 31, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003778187.2

Allele description [Variation Report for NM_006164.5(NFE2L2):c.445G>A (p.Gly149Ser)]

NM_006164.5(NFE2L2):c.445G>A (p.Gly149Ser)

Gene:

NFE2L2:NFE2 like bZIP transcription factor 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q31.2

Genomic location:

Preferred name:

NM_006164.5(NFE2L2):c.445G>A (p.Gly149Ser)

HGVS:

NC_000002.12:g.177232541C>T
NM_001145412.3:c.397G>A
NM_001145413.3:c.376G>A
NM_001313900.1:c.397G>A
NM_001313901.1:c.397G>A
NM_001313902.2:c.355G>A
NM_001313903.2:c.226G>A
NM_001313904.1:c.145G>A
NM_006164.5:c.445G>AMANE SELECT
NP_001138884.1:p.Gly133Ser
NP_001138885.1:p.Gly126Ser
NP_001300829.1:p.Gly133Ser
NP_001300830.1:p.Gly133Ser
NP_001300831.1:p.Gly119Ser
NP_001300832.1:p.Gly76Ser
NP_001300833.1:p.Gly49Ser
NP_006155.2:p.Gly149Ser
NC_000002.11:g.178097269C>T
NM_006164.4:c.445G>A

Protein change:

G119S

Molecular consequence:

NM_001145412.3:c.397G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001145413.3:c.376G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001313900.1:c.397G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001313901.1:c.397G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001313902.2:c.355G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001313903.2:c.226G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001313904.1:c.145G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006164.5:c.445G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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SAMN44298493 (1)
SRA
PREDICTED: Rattus norvegicus Ral GEF with PH domain and SH3 binding motif 2 (Ral...
PREDICTED: Rattus norvegicus Ral GEF with PH domain and SH3 binding motif 2 (Ralgps2), transcript variant X1, mRNA
gi|2678891782|ref|XM_039090753.2|

Nucleotide
aldehyde dehydrogenase family 3 member B1 [Mus musculus]
aldehyde dehydrogenase family 3 member B1 [Mus musculus]
gi|34328288|ref|NP_080592.2|

Protein
RecName: Full=Glutathione S-transferase Y1; AltName: Full=Chain 3; AltName: Full...
RecName: Full=Glutathione S-transferase Y1; AltName: Full=Chain 3; AltName: Full=GST class-mu
gi|399829|sp|Q00285.2|GSTMU_CRILO

Protein
RecName: Full=Proteinase-activated receptor 1; Short=PAR-1; AltName: Full=Thromb...
RecName: Full=Proteinase-activated receptor 1; Short=PAR-1; AltName: Full=Thrombin receptor; Flags: Precursor
gi|2506485|sp|Q00991.2|PAR1_CRILO

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004625155	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 31, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004625155

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 31, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004625155.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. This variant has not been reported in the literature in individuals affected with NFE2L2-related conditions. This variant is present in population databases (rs371179136, gnomAD 0.007%). This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 149 of the NFE2L2 protein (p.Gly149Ser).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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